Variant report

Variant	rs1519813
Chromosome Location	chr8:121060884-121060885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr8:121060698-121061042	HepG2	liver:	n/a	chr8:121060856-121060871
2	FOXA1	chr8:121060718-121061006	HepG2	liver:	n/a	chr8:121060856-121060871
3	POLR2A	chr8:121060282-121061041	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOXA1	chr8:121060699-121061009	HepG2	liver:	n/a	chr8:121060856-121060871
5	FOXA2	chr8:121060670-121061018	HepG2	liver:	n/a	n/a
6	FOXA1	chr8:121060725-121061007	T-47D	breast:	n/a	chr8:121060856-121060871
7	FOXA1	chr8:121060623-121061109	HepG2	liver:	n/a	chr8:121060856-121060871
8	JUND	chr8:121060327-121061040	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000254343	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10090001	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10095205	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10095532	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101620	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10101943	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10505376	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10808506	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs10955948	0.86[EUR][1000 genomes]
rs1120223	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11780912	0.86[EUR][1000 genomes]
rs11780985	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12114445	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12542895	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12543907	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12545676	0.85[EUR][1000 genomes]
rs12548273	0.86[EUR][1000 genomes]
rs1519807	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1519808	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1519812	0.81[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap]
rs16893478	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16893517	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17226296	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs1980228	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292946	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28530768	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2875928	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2875931	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4871825	0.84[GIH][hapmap]
rs4871828	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56702755	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57868486	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60717250	0.86[EUR][1000 genomes]
rs60754245	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6469894	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6469895	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6469897	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66490854	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66507952	0.83[EUR][1000 genomes]
rs66614869	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67872361	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980708	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6986231	0.85[EUR][1000 genomes]
rs6993924	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6998730	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7004815	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7005228	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7007998	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7013298	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7016816	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73315941	0.86[EUR][1000 genomes]
rs7817016	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7820543	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7821947	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7822662	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7822927	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7824793	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7829101	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7829116	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7830028	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7833073	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7836087	0.82[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7841230	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7841621	0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7843503	0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs955293	0.88[ASW][hapmap];0.84[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs960887	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3348294	chr8:121000288-121250984	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1519813	DEPDC6	cis	uninvolved skin	skin_eQTL
rs1519813	RP11-760H22.2	cis	Adipose Subcutaneous	GTEx
rs1519813	DEPDC6	cis	normal skin	skin_eQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121017000-121067000	Weak transcription	Brain Anterior Caudate	brain
2	chr8:121022400-121065400	Weak transcription	Left Ventricle	heart
3	chr8:121036000-121063800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr8:121038400-121061800	Weak transcription	Adipose Nuclei	Adipose
5	chr8:121042000-121063400	Weak transcription	Spleen	Spleen
6	chr8:121046200-121065200	Weak transcription	Psoas Muscle	Psoas
7	chr8:121048600-121061800	Weak transcription	Fetal Intestine Large	intestine
8	chr8:121048600-121061800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr8:121048800-121063600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr8:121048800-121063600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr8:121049200-121062200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr8:121049200-121072800	Weak transcription	Fetal Lung	lung
13	chr8:121049200-121072800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr8:121053600-121064000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr8:121053600-121067200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr8:121053600-121072800	Weak transcription	Brain Angular Gyrus	brain
17	chr8:121053600-121072800	Weak transcription	Brain Substantia Nigra	brain
18	chr8:121053600-121072800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr8:121053800-121072800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr8:121054600-121061800	Weak transcription	Brain Hippocampus Middle	brain
21	chr8:121054600-121061800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr8:121057400-121061800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr8:121058400-121065400	Weak transcription	Pancreas	Pancrea
24	chr8:121058400-121066200	Weak transcription	Gastric	stomach
25	chr8:121058600-121061600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr8:121059200-121061800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr8:121059400-121077800	Weak transcription	Fetal Stomach	stomach
28	chr8:121059600-121064600	Weak transcription	Fetal Intestine Small	intestine
29	chr8:121060000-121061000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr8:121060000-121061000	Enhancers	Ovary	ovary
31	chr8:121060000-121062600	Enhancers	H1 Cell Line	embryonic stem cell
32	chr8:121060200-121061000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr8:121060200-121061000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr8:121060200-121061200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr8:121060200-121062600	Enhancers	Liver	Liver
36	chr8:121060400-121061000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr8:121060400-121061000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr8:121060400-121061000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr8:121060400-121061000	Enhancers	HepG2	liver
40	chr8:121060400-121061200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr8:121060600-121061000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr8:121060600-121061000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr8:121060600-121061000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr8:121060600-121061200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr8:121060600-121061200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr8:121060600-121063600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr8:121060600-121064400	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr8:121060600-121085000	Weak transcription	Fetal Muscle Leg	muscle
49	chr8:121060800-121061000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr8:121060800-121061000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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